What if?
by Appo's avenger
Summary: This is my first piece of writing so I hope you enjoy it. The Clones removed their Biochips that was intended for them to execute order 66. I will be following the canon (at best ;) and adding a few new parts. If you have any characters you would like to see in the story please tell me. Please note: I don't own Star Wars or the Characters (I wish I did)
1. Chapter 1

Star Wars

What if?

Chapter 1

New Enemies

 **Shortly after the incident with ARC trooper "Fives", the biochips implanted within all clone troopers became known to Captain Rex. He warned all other Clone officers to remove them before Chancellor Palpatine ordered Protocol Order 66 in which clones were to execute their Jedi Commander.**

On Utapau

Commander Cody, Lieutenant Boil and the 212th Attack Battalion were in the process of removing their biochips. Long queues of the orange-marked troopers scribbled across Pau City, slowly decreasing as they moved among the fallen battle droids. During the process, Cody approached General Kenobi, a Jedi Master and recently responsible for the death of the cyborg General of the CIS General Grievous.

"Sir, the Seps have been pushed into the Lower Levels of the city, and most of the troopers have removed their chips already" Said Cody, in the most enthusiastic manner

"Very good Cody. We will have the planet in no time" Kenobi proclaimed

As Kenobi began to walk off, Cody exclaimed: "You are going to need this, Sir" Said Cody as he handed the Jedi his lightsaber.

"The 212th are right behind you sir" Said Cody proclaiming his, and his soldiers, loyalty to the Jedi order.

Mygeeto

A clone trooper, clad in the standard Galactic Marine armor, appeared on a hologram to Commander Bacara. The trooper stated: "All troopers of 21st Nova Corps removed their biochips sir". Commander Bacara headed towards Jedi General Ki-Adi-Mundi to inform him about this.

"The troopers are free from the control of the Chancellor" said Bacara. He was a skilled soldier and brilliant tactician, always placing his troopers first.

"Excellent Commander. Let's free this planet and meet up with the rest of Jedi"

Saleucami

Commander Neyo exited the infirmary after removing his biochip. Lieutenant Limb approached Neyo. Limb earned his nickname after he tore apart a battle droid limb from limb, his ferocity in battle earned him his rank. 'All troopers are about to remove their chips sir'. Neyo responded in the same voice. A voice that millions of other clones have.

'Excellent. Inform the General. Contact the fleet, as soon as we finished here, we are leaving'

* * *

Corascant

Commander Appo and Captain Rex walked through the Jedi temple, ordering troopers and evacuating the Jedi. The Jedi were leaving behind their temple, their home and symbol of their order. Eeth Koth assumed control of the evacuation, ordering clones and calming down the few panicking Jedi. The 501st was loading the Jedi onto LAATs that were taking them into orbit and carrying various objects such as clothing, books, and most importantly the sacred Jedi holocrons. The holocrons contained the teachings of the Jedi order and carried the most closely guarded secrets of the order.

Mace Windu, Jedi master and current head of the order, gathered a task force that was intended to arrest Palpatine, abandoning the evacuation and the many younglings. Two LAAT gunships ferried the task force, consisting of the Jedi Kit Fisto, Seasee Tinn and Agen Kolar as well as Commander Appo and a squad of troopers, to the senate building which housed the Chancellors Office.

They arrived in the lobby of the office and Appo told a trooper to stand guard as the rest of the force entered the main office. "I assume General Grievous has been killed and Utapau has been liberated" stated the elderly Palpatine, trying to sound sincere.

"In the name of the Galactic Senate of the Republic, you are under arrest. We know of your plot to undermine the Senate and execute the Jedi" Said Windu in a strong and determined voice.

The Jedi ignited their lightsabers and the clones surrounded the Chancellor. Appo and his men levelled their blasters to his head.

"Surrender now sir, you are outnumbered," stated Appo

Palpatine let out a sinister laugh and pulled out his own crimson coloured lightsaber. He leapt up and began to cut-up the troopers, hacking and slashing at them. The troopers tried to defend themselves, but all attempts were in vain. Appo retreated to the entrance, fearing for his life, as the Jedi began their duel with the now known Sith Lord.

Palpatine leapt towards the Jedi, letting out a sinister battle cry, one that had not been heard since the old Jedi-Sith wars. He quickly placed his blade into Kolars chest, who was caught with his lightsaber above his head as if he were to strike Palpatine down. He quickly spun around to disembowel Tinn, who also had his guard down. Windu was surprised by his speed. His agility. His skill. Windu blocked his attacks and Fisto began his attack as the Sith Lord as defended with immense skill.

During the Duel, Appo, the last trooper standing, fired a few shots in an attempt to avenge his fallen comrades and end this whole thing right now. His shots hit and broke the large window at the rear of the office. Palpatine, saw an opening during the duel and force blasted Kit into the wall, shattering every bone in his body, leaving Windu to defend himself against the very skilled Sith.

The final duel between Windu and Palpatine had taken place, in which Mace blocked all assaults made by the Sith Lord. Appo kept trying to assist but feared of hitting the Jedi. Windu eventually broke the Sith's defence and he fell to the ground. He crawled to the broken window and braced his back against the wall that previously held the window in place.

"You will never overthrow the Senate!" exclaimed the Jedi

"I am the Senate" stated the old gravelly voice

At the same time Anakin Skywalker walked into the lobby and found the clone trooper who waved Anakin straight through into the office, believing he was going to assist in the arrest. Anakin walked straight into the main office and found Appo, an officer in his army, Mace Windu, his Jedi master, and Chancellor Palpatine, whom he greatly admired. Anakin developed a close relationship with Palpatine, after the Sith Lord promised to save his wife from a vision he had, in which Padme dies. He also found the bodies of Jedi masters and several clone troopers.

"Palpatine … Palpatine is trying to overthrow the Republic. He tried to kill all Jedi using biochips in the clones. He is the … the Sith Lord''

"Chancellor, is this true?"

"No Anakin, He is a liar! The Jedi are traitors to the Republic"

"Now you die Sith Lord!" Exclaimed the Jedi

"No, no...NO!"

Palpatine let out lightning from his fingertips, a power only the greatest of Sith could wield. Windu deflected it back towards him with his weapon. Unfortunately, some of the current flowed through his lightsaber and into his body.

"Anakin help… me. He seeks to destroy the Republic and the Order"

"My allegiance is to the Chancellor not the Order"

Appo raised his blaster to Palpatine. Anakin turned and Force pushed Appo out the window. Anakin then moved towards the two engaged in a power struggle.

"Don't listen to him Anakin!" screeched Palpatine.

Eventually, Palpatine stopped letting out the lightning and laid against wall, badly deformed from the deflected lightning. Windu lifted his weapon towards Palatine's head.

"You are under arrest, my lord" Said Windu, sarcastically.

"You cannot kill him!" Exclaimed Anakin

"He is too dangerous to be left alive. He controls the Courts and the Senate!"

"Don't let him kill me Anakin!" The grave voice sounded like it was already dying

"The oppression of the Sith will never return" Said Windu just as he raised his lightsaber to strike him down.

"I can save your family!" Screamed Palpatine, trying to convince Anakin to help him.

"Yes Anakin give into your hate. Give in to the Darkside" Palpatine let out a dark and sinister laugh.

In one quick strike, Anakin ignited his lightsaber and decapitated the Jedi master.

"What…What have I done" Said Anakin, thinking of his actions. He fell back towards a desk, braced himself against it and ran his hands across his face

"You are fulfilling your destiny! Become my apprentice and learn the ways of the Darkside"

"I cannot!"

"Give in to hate and anger, it makes you stronger! You can save her, but only through me and the Darkside" He laughed

"Rise now as Darth Vader" He let out another laugh

"Now, go to the Temple and kill every Jedi!"

"It shall be done, master"

Palpatine gave out another laugh, more sinister than the last.

The clone trooper on guard outside made for an escape after he heard of this. He got to the LAAT and left immediately for the Temple.

* * *

Meanwhile…

The Jedi gathered their various armies and fleets, and congregated on the planet of Bardotta, where the natives where extremely force sensitive and loyal to Jedi. The various fleets of Aayla Secura and the 327th Star Corps, Ki-Adi-Mundi and the 21st Nova Corps, Plo Koon and the 104th Battalion, Luminara Unduli, Quilan Vos and Yoda with the 41st Elite Corps, Obi Wan Kenobi and the 7th Sky Corps, Stass Allie and the 91st Reconnaissance Corps and Rahm Kota and his private militia met up on Bardotta. Kota never trusted the clones, so he set up his own militia instead. He feared something like this might happen, the clones turning on their Jedi commanders. More and more Jedi gathered and a temporary Council was set up.

On the surface, the new council convened in an old Jedi temple, and consisted of Secura, Unduli, Yoda, Kenobi, Mundi, Koon and Eeth Koth who was still on Corascant. At the same time, all Clone Officers met outside the temple.

"I can't believe we were supposed to kill the Jedi" Said Gree, Luminara Unduli's commander, still in disbelief if the reason he was created

"What of Commander Thire, have we heard anything from him" Said Wolffe, a true definition of a veteran soldier, completely ignoring Gree statement of concern

"Nothing yet. I don't think they removed their chips, they are fiercely loyal to the Chancellor and have no Jedi commander, so killing them won't be a problem" Bacara stated

"Bly, what about Appo and Rex, have they evacuated the temple yet" Asked Cody

"The last we spoke, Appo was heading to arrest Palpatine" Replied Bly


	2. Chapter 2

Star Wars

What if?

Chapter 2

Unexpected Reinforcements

 **After the death Mace Windu, Anakin Skywalker, now known as Darth Vader, plans to assault the Jedi Temple and start The Great Jedi Purge. The remaining Jedi plan to evacuate before the attack.**

Corascant

Commander Thire and his Shock troopers marched, with Vader leading them, to the Jedi temple. The elite red-painted troopers walked up the steps of the temple. The trooper that witnessed the incident at the Chancellors Office managed to reach the temple in time, to warn the Jedi.

Eeth Koth set up the defenses, ordering the Jedi and clones alike. All younglings were to go to the hangar, the clones were set up a barrier in the Main Hall. Those that have not yet being evacuated, would have to defend the temple until they could be evacuated.

Once the barriers were set up, a few turrets were set in place and all younglings in the hangar bay, they were ready for the assault. The clones took up positions behind their barriers of crates, broken down pillars and rubble, and laid in wait to defend the Jedi from their own brothers. They were about to fight men that they fought with side by side to stop the tyranny that now control them.

Commander Rex, now promoted due to Appo's death, was on the front line of the defense. He was always leading from the front. The Shock troopers advanced to the entrance of the Temple. Marching in a constant formation. With Vader at the front. The 501st knew what they were facing. There was deep silence in the whole temple. It was disrupted by sound of blaster fire coming from the entrance and the barriers. Deadly blue bolts were exchanged. The Shock Troopers took cover behind the columns of stone at the entrance. A squad of Shock Troopers armed with riot shields entered the conflict, providing a source of mobile cover for the advancing troopers. Anakin entered the fighting deflecting the shots towards his former troopers.

The Jedi jumped up from behind their cover and fought back, deflecting shots in a similar manner to that of their former Jedi colleague. The Shock Troopers advanced taking few casualties compared to that of the defending army, giving off immense firepower, trying to break their brother's defense.

"Rex, how much longer till the gunships get here!" Exclaimed Koth, trying hard not to be drowned out by sounds of war while at the same time deflecting blaster fire back at the invaders

"Not long sir! E.T.A. five minutes!" Screamed the Clone Commander

The battle raged on as the Shock Troopers advanced further and further getting closer to the barriers of their adversaries. Thermal detonators were tossed towards the cover of the 501st, exploding and killing many. The 501st were taken heavy casualties, and even a few Jedi fell by the blaster fire. The blue lightsaber on the side of the Shock Troopers retreated from the fight.

"Sir, the gunships are here!" Exclaimed Rex

"Good! Let's get out of here! I will cover your retreat" Screamed Koth

"Yes sir! Everyone, we are leaving!" Ordered Rex

The Troopers retreated from their cover heading toward their second line of defense. The Jedi too retreated, deflecting the fire coming from the ever advancing Shock Troopers. The battle moved to the inner corridors of the Temple, with squads of troopers and Jedi working towards the Hangar.

The gunships arrived at the hanger with their blast doors closed. The doors opened and Vader walked out. The younglings ran up too him, unaware of his darkside change.

"Master Skywalker! We were told to wait for the gunships" one of them announced

Vader ignited his lightsaber

Sometime later

The troopers and Jedi made their way to the hanger, and was halted by shock. There was no gunship, but there was the lifeless bodies of the younglings and a large group of Shock Troopers accompanied by Vader. The 501st took cover behind Starfighters and crates of various clothing. The Jedi ignited their lightsabers. Green and blue hued weapons stood at the entrance to the hanger. Koth stepped forward, voicelessly challenging Vader.

Again, blaster fire was exchanged, hues deflecting bolts back to their origin. Vader and Koth began their duel, Koth making the first strike to Vader's weapon. The duel continued, both parties seemingly ignoring the war going on around them, dancing in the center of the hanger, continuously trying to break the defense.

The original group of Shock troopers pushed through the second line of defense inside the temple, slaughtering the few brave blue painted clones who decided to make a last stand against their brothers. The battle was almost lost for the defenders as Shock Troopers attacked from exit of the hanger. There was no retreat for Jedi, the 501st fell by the blaster of the clearly superior troopers.

A sound roared through hanger as a ship, resembling a Correlian G9 rigger Freighter, approached the exit, a hooded figure appeared in the cockpit. The sound halted the dance of the two hues in the center of the hanger. More noise came about as the ships laser cannons opened fire upon the Shock Troopers, bringing them down and ultimately stopping the firefight.

The 501st cheered for their unknown reinforcements, as well as the deaths of their now hated brothers. Several LAAT's entered the hanger to carry the Survivors away. The ship spun around and the rampart opened, the pilot stood waiting as it opened. The clones and Jedi' eyes were met by a familiar sight. Ahsoka Tano, Vader's former padawan and former Jedi, called out to the Jedi.

"Get aboard the ship, now!" she ordered

"You heard her! Move out!" Rex yelled to Jedi and Clones

The main duel continued as the survivors ran past and entered their transports. The lightsabers clashed in the center of the hanger with Koth nimbly dodged assaults and attempted to break Vader's defense.

"Master Koth!" Screamed Tano

"Go, I will hold him off!" He replied

Vader and his opponent eventually got caught up in a power struggle, with each other trying to break their opponent's defense.

"How could you kill younglings Skywalker?!" Screeched the Jedi Master

"You are weak Master Jedi! I expected more from you" Replied Vader

In a quick swoop, Vader placed his blade in the Jedi's chest. He let out a cry as he felt Death upon him. Vader lifted the still live body to his face and whispered to the near-corpse Jedi

"I don't only kill younglings" with that said, Death carried the Master Jedi away

He dropped the now lifeless body of Jedi Master Eeth Koth. Ahsoka watched in horror as her former master killed a Jedi. Anakin was now truly gone, the Darkside consumed him. Vader turned to the ship as the last few Jedi and injured clones were being loaded. Rex and his men opened fire in an attempt to delay the Sith Lord. All attempts were in vain as the shots were reflected elsewhere in the hanger.

The transports eventually took off leaving Vader starring at them. Vader watched as his former compatriots escaped his grasp. The Shock Troopers eventually broke into the hanger, only to find their former clone brothers and Jedi commanders missing. The Shock Troopers rushed past Vader, some to the edge of the hanger, others to their injured brethren.

"Thire, contact the fleet. Order them to shoot down any thing that tries to leave the planet!" Vader ordered

"Yes sir!"

Later, On the _Veracity_

"Admiral, make the jump to hyperspace!"

"Yes sir. Engaging Hyperdrive"

The ship rocked to side as more fire from the other cruisers hit it

"We can't take much more of this Admiral!"

"All ships, make the jump now!" Ordered the Admiral

All Starfighter turned around, leaving their fights and pointed towards the collective direction of all 'Traitorous' vessels. The vessels stretched into space and jumped to hyperspace. The white light zoomed pass the vessels as they traveled through space.

"Close one, Admiral"

"Indeed Commander Tano. We will meet up with the rest of the Jedi in approximately two hours"

"Thank you Admiral"

Ahsoka left the bridge to meet up with Commander Rex. Three Venator Class Star Destroyers as well as hundreds of Starfighters left Corascant, they all headed towards Bardotta.

"Rex!" Ahsoka screamed as she met her former comrade

"Commander Tano, I didn't expect us to survive that one. Thank you" He said as he embraced her hug

"The men aren't looking good sir" Rex stated as he removed his helmet

"We took heavy casualties, so many good men were lost" Rex stated again

"We can combine the forces of yours and the 698th battalion"

"Good idea sir. Were they not the men that fought on Dac?"

"They did, very brave men. I am sure you have met with Commander Nexu"

"I doubt I have"

Their conversation continued as there headed towards the main hangar to meet with Commander Nexu, Kit Fisto's former commander. They discussed many things, except the new Sith Lord. They eventually reached the hanger and a green and yellow painted trooper with a check green and yellow Kama, yellow pauldron and macrobinoculars raised to the top of his helmet. He noticed them coming and raised himself from his sitting position.

"Commander Tano, what do you require" Nexu stated

"This is Cap-, sorry, Commander Rex of the 501st. We were hoping your Battalion would join up with Rex and his men" Ahsoka stated, quickly correcting her mistake

"Well, we would be happy to. But, I wish to keep my battalions colors, in honor of General Fisto. He personally picked them." Nexu requested

"You may. Ill introduce you to the men. It will be good to replenish my troops, and have another brain to help out with strategy." Rex stated, smiling beneath his helmet

"Thank you Rex"

Rex raised his communicator towards his head and spoke

"Jesse, get Fives and the men down here, we got good news"

A voice returned through the communicator

"Yes sir, we one our way!"

Moments later several 501st ARC troopers, Including Jesse and Fives, and officers approached.

"Listen up men!" Rex announced

"The 698th will be joining our ranks" Rex said as Nexu and his men lined up behind him

"This is Commander Nexu. You will treat him with the same respect as you treat me" Nexu stepped forward next to Rex

"His men will be your brothers, you will fight with and for them wherever and whenever. They are now members of the 501st."

"Yes sir!" The officers said

The officers moved towards Nexu and his men.

 **How was that. Please comment and review. I will be releasing the next chapter soon.**


	3. Chapter 3

Star Wars

What if?

Chapter 3

Return to Corascant

 **Death of Eeth Koth, by Darth Vader, was mourned by the Jedi order. A plan to infiltrate Corascant by Jedi a clone commandos was being formulated. A plan to destroy the Sith, and save the republic.**

Bardotta

"Bacara, where is your squad? We are moving out in a few minutes." Ki-Adi-Mundi asked while he checked his equipment

"They are on their way. Three ARCs and my Captain, Sir!" Bacara snapped

Bacara, Cody, Rex, Nexu, and Wolffe were joining their Jedi Commanders on their mission. Each Commander set up small squads to accompany them to Corascant. After a few minutes, the strike force was ready. Their Transports arrived to take the force to Senator Organa's ship which was in orbit.

"Master Yoda, the ships are here. We are ready to leave" Nexu told the small master

"Excellent Commander. Contact Senator Organa, prepare for our arrival he must."

"Yes sir." The Clone responded

The task force were taken to Senator Organa ship in orbit. Once there, everyone met up in one room, with a long, white table down the middle with twenty orb shaped seats around it. The Clones arrived before everyone else. They waited for a few minutes for the Jedi and Organa to arrive. There was complete silence in the room before Obi Wan opened up the meeting.

"The Jedi are to head to the temple." He stated calmly

"Bacara, you and Wolffe are coming with us to the temple. Rex, take your squad to the Senate. Try to find Sympathisers for our cause and find Senator Amidala. Cody-" Obi wan was interrupted by the sound of the doors opening. Ahsoka walked through and the meeting was interrupted.

"Ahsoka, you were supposed to stay on Bardotta" Plo Koon stated calmly, with his hands interlocked on the table

"I'm sorry masters. I had to come with, I have to help you" She pleaded to the meeting. There was a moment of pause where the Jedi looked at each other but the clones had their eyes fixed on Ahsoka

"Ahsoka, go with Rex to the senate, gather support you must" Yoda stated

"The Republic has completely changed." Organa stated as he listened to his communicator. Everyone looked at him and waited for his follow up

"It's being transformed into the Galactic Empire. Palpatine declared himself Emperor. He is conscripting people from Corascant to rebuild his armies. He named the Jedi and Clones outlaws, which will be hunted down and killed" He said. There was a slight tone of worry in his voice.

"Confront Palpatine, I will. Cody, to his office, your squad, will take me"

"Yes Sir. I have plan to enter undetected, but I don't think you going to like it"

"So we all have our parts to play" Ki Adi Mundi said proclaiming the end of the meeting

The ship jerked into hyperspace towards Corascant. Everyone headed to their quarters to prep for their upcoming mission. The Clone Commanders all gathered in a room within the ship. They were playing Sabacc, discussing the mission, when two ARC troopers walked in, Duke and Kix. Both clad in full armour, sat down around the table next to their brothers, they removed their helmets like the others and placed them on the floor next to them

"Something wrong Kix?" Cody asked, noticing a look of worry on his face

"No Sir!" He replied

"Relax, Kix. We are all brothers here, no need to call us 'Sir'." Wolffe said, air quoting his words

Duke turned his head to his Commander, Bacara

"Bacara, may I ask you a question"

"You may" Bacara replied, with his eyes locked on his cards

"Sir, Kix and I are worried about the mission. We heard what Palpatine could do. He killed four Jedi Masters and Appo, what's stopping him from killing the Jedi with us. What if he-" His words came to an abrupt end by Bacara. He completely changed the mood of the gathering

"Duke, relax. The Jedi know what they are doing, and we know what we are doing. We will bring an end to this, once and for all. Now relax, stop worrying" Bacara tried to bring the mood down and calm the situation. The clones looked at one another, confused as why a Galactic Marine, one of the best units in the Republic, was scared of Palpatine.

The game continued, but the thought of Palpatine killing all the Jedi still lingered in the air. Eventually, Wolffe was declared winner and everyone went to their respective quarters and fell asleep. Thoughts wondered throughout the ship, the future, the Jedi, the Sith, the new Empire. All minds thinking, worrying, dreaming.

The ship jerked out of hyperspace and the stars began to take shape again. Corascant appeared, the lights of the planet slightly blinding, the Home Defence Fleet appeared. Venators. Countless in number. Two ARC-170 fighters appeared alongside the cruiser. The Captain of the cruiser communicated with the Admiral of the fleet. The Ship was allowed through and the fighters moved away. The strike force was woken up. The ship moved towards the planet.

The ramp opened, clones and Jedi stormed out. Several airspeeders were already waiting. Boots scratched across the surface of the landing pad. Teams of six entered their speeders. Silence was held by everyone, two separated from the rest of the group, and the main group found their way to the Jedi temple. The Jedi exited the speeders first. They ignited their weapons as they saw Shock troopers exit the temple. Wolffe shot first, opening up the battle.

The force made their way through the Temple, towards the security room, to catch a glimpse to where Vader left for. They ran past bodies of clones and Jedi, occasionally fighting off Shock Troopers.

"Master Kenobi. A perimeter has been set up, Boost will get to work on the Security Feeds immediately."

"Excellent Wolffe. Get your team to accompany Master Plo to the Archives to retrieve any data we left during the evacuation"

"Yes sir"

Wolffe walked off a little bit before turning around and rushing back to Kenobi

"Sir! Rex has found Senator Amidala. Rex said she is pregnant, they on route to Senator Organa ship."

"Very well. What of Cody and Master Yoda"

Meanwhile…

"Sir, we have reached maximum altitude height, we are ready to make the jump"

"Excellent Commander" The small Jedi replied

"Hold on to me Sir, Cody will circle around to pick us up"

Wooley, Boil and Yoda jumped from the airspeeder. They fell through the traffic and speeders moving past them. They came close to the Senate building and activated their Jetpacks. The three figures floated down to the building elegantly. They landed and moved to an area above Palatine's office, Yoda pulled out his Lightsaber and began cutting a hole in the roof.

"Master Yoda, activate your Homing beacon when you are ready"

"Thank you Wooley and Boil"

"May the force be with you Master Yoda"

Yoda fell into the hole and the clones worked their way down to the hanger bay.

Back at the Temple

Bacara's communicator buzzed

"Bacara, we need assistance in the library, we being pushed back by 'Storm Troopers'." The sound of blasters being fired were going on in the back round

"Copy that Wolffe, we on our way"

Kenobi and his men, after knowing the whereabouts of Anakin, headed towards the library. They found Plo and Wolffe fighting off, white armoured, troopers. The Jedi began to pull out as Sinker and Comet were carrying the last of the holocrons. They rushed to their airspeeders back to where they came. They left the Temple for the final time, as Storm Troopers fired off shots trying to bring them down.

Elsewhere on Corascant

"Commander Cody, ready I am"

"Yes sir, I am on route to your location now"

After waiting a bit, Yoda dropped into the airspeeder. He found Cody, Wooley and Boil inside.

"Failed, I Have"

The team met up with everyone else at Organa's Ship. Rex and Nexu were talking on the landing pad, Mundi, who was walking up the ramp turned to see the diminutive Jedi Master.

"Leave we must. Sense much danger here I do"

"Yes master, I will inform Senator Organa"

The ship lifted off the ground and left the planet, probably the last time the Jedi would see their Temple. The ship jerked into hyperspace again, towards Bardotta. Everyone, with the addition of a Senate Commando and Senate Guard squad, met again in the meeting room. Rex opened the meeting this time.

"We managed to get support from some senators, with the addition of Commander Zackery and Commander Taggart, of the Senate Guard" There was a pause as the two Commanders stepped forward, one of which was still in the ceremonial guard armour and the other in commando.

"There was a plot to phase out the Guards, and destroy democracy. Our allegiance is to those who defend it, Rex told us about you. The rest of the Guard will be leaving Corascant shortly"

"Thank you for your support Commander Zackery" Kenobi said

"Kenobi, what of Skywalker, to where has he gone"

"To the Mustafar system, master Yoda"

"And Senator Amidala" Mundi requested, ever seeking knowledge. Kix stepped forward to answer the question

"She is stable sir. She might go in to labour soon"

"Anakin the Father is" Yoda stated

"Kenobi, find Anakin you must. Try to save him you will"

A sound buzzed on Bacara's communicator

"Incoming transmission from Master Unduli"

"Put her through" Kenobi ordered

A hologram appeared in the centre of the table, perfectly facing Yoda.

"Master Yoda, The Bardottans" There was a pause as the Jedi moved towards Yoda to get a better view of Unduli

"They want us off planet. They fear we would bring war to Bardotta. What are we to do?"

"Correct the Bardottans are. A war is coming. Move to Dantooine we must, safe it is, far away from the Empires reach it is"

"I agree master Yoda, but what of the Clones. If a war is coming our troops must be able to fight it. The growth acceleration needs to be stopped. The Clones are ageing, eventually they will be too old to fight" Mundi stated with concern

"Retrieve the Kaminoans, you must. Take Padawan Tano and Master Kota with you, find a cure you must, and turn Kota's view on the Clones. To Geonosis Mundi and I will go, much fear do I feel there. Everyone else to Dantooine will go, rebuild the Temple there we will"

The meeting ended and everyone returned to their quarters. They fell asleep as the ship lightly rocked through space. Padme lied on her bed, awake, but her eyes were closed. She struggled to sleep, rolling over to each side, she knew what was coming.


	4. Chapter 4

Star Wars

What if?

Chapter 4

Confrontation

 **Failure to defeat Palpatine, Master Yoda assigned the Jedi tasks, including the rebuilding of the temple on Dantooine. Obi Wan Kenobi is heading to Mustafar, to defeat his former apprentice.**

"General Kenobi, we will reach Mustafar in a few minutes. Reports say there is no Imperial or Separatist presence in the system"

"Excellent Cody, ready up a Gunship for me" He ordered

"Yes sir!" Cody snapped

The fleet of Venators, dropped out of hyperspace. The red and orange of the massive lava lakes and rivers appeared on the planet. Mustafar. Kenobi felt the darkness on the planet. It was strong.

A lone LAAT floated down to the surface, landing in one of the hangers of one of the countless mining facilities. Kenobi stepped out as the blast doors opened. He moved towards the entrance of the facility.

He walked into a meeting room, and to his surprise, he found the lifeless bodies of separatist leaders. Lightsaber wounds on all the bodies. The doors on the opposite end of the room opened. Anakin walked out.

On Kamino

Clones and Militia battled on Tipoca City. Rahm Kota, Plo Koon, and Ahsoka Tano, battled Storm Troopers, through corridors, rooms, and hangers.

"General Kota. We've pushed the Imperial back. Me and Wolffe have-" The holograms words stopped as Kota turned his communicator off. He hated hearing the success of Clones.

The group of Jedi stopped to rest in one of the blinding white corridors. They were accompanied by a squad of Militia. Some sat with their backs against the wall, others stood with their blasters raised, and others checked their equipment. Ahsoka approached Kota, who was standing, with his arms folded, grimly looking at the end of the corridor.

"You should really trust the clones, Master Kota. They are good men"

"I would never trust them, they nearly killed us all"

"But they didn't"

"This conversation is over, padawan" A patronizing tone reeked in his voice. He walked off leaving Tano, starring at his back.

"Ahsoka, Master Kota will find his own view of the Clones. You cannot force it" A deep voice surprised her from behind. She turned to find Plo.

"I know Master. Why can't he just see they are good loyal men"

"Patience, Ahsoka. Now let's move out, Wolffe might need assistance"

The Squad walked off down the corridor, blasters raised, ever prepared for battle.

Mustafar

"Cody, send a gunship. I'm done here" He walked off, leaving Anakin, missing his last organic limbs, steaming on a lava bend.

"I HATE YOU!" Vader screamed at Kenobi. Vader only slipped further down, trying to climb up with his mechanical hand, the bend and got too close to the lava stream. Orange and yellow tongues covered the torso of Vader, moans and groans and screams came from him as he burnt. His body lye there, the shell of what was The Chosen One, the one that would bring balance to the force.

The Venators jumped into hyperspace. Three other vessels took their place, grey in color but similar in shape. Imperials. Palpatine. A Lambda class shuttle left one of the ships. Moments later, Palpatine walked down the ramp, flanked by Red Guards and followed by a squad of Shock Troopers.

"Your majesty, this way!" one of the troopers exclaimed

"There he is—he's still alive. Get a medical capsule, immediately."

"Yes, sir. Right away." He ran off leaving, Palpatine kneeling over Vader

On Kamino

"Master Kota look out!" A voice cried out

Kota lifted his head upwards to a falling beam. He felt his body jerk over, moving out of the way of the beam. He found his body underneath a clone trooper. Boost tackled him out of the way, saving his life. Boost immediately got up, lowered his hand to Kota, still dazed. Kota grabbed it and lifted himself up, he starred at Boost, he saw beneath his helmet. Boost in confusion of the Jedi staring at him, quickly snapped a salute.

"Thank you" Gratitude mixed with confusion and embarrassment

"You welcome sir!" The reply came swift

Plo and Ahsoka looked at each other. A conversation was about to start but the battle would not permit it. Blaster fire, blue and red. The Storm Troopers, making a last stand took cover behind a crates and boxes. For a brief moment there was no blaster fire, but then the blue beams continued.

"Stop! Hold your Fire!" Kota ordered

The Clones and Militia complied and the Storm Troopers stood up. The White Clad soldiers raised their hands, above their heads. The Clones rushed forward, and raised their blasters. Stun Cuffs were placed one the new prisoners. Dan Barr, the commander of Kota's Militia approached one of the prisoners.

"Where is your Commander?" He asked

"We don't talk to rebel scum like you" The voice retorted through its helmet

"He must be the Commander then" Plo stated as he moved into the group

Plo had a thing for reading minds. He and Kenobi mastered it, among other things. The wonder that is the force saved his life on many occasions. He felt something in the force. Something dark, something irregular. He jerked over to the side, raising his head to Kota

"I feel it too" Kota said

"We need to meditate on this. Wolffe, wrap this up and meet us back at the ships. Ahsoka, stay with them"

"Yes sir. Comet, Boost, get the prisoners to the brig" Wolffe ordered

Kota and Koon walked back to the ship, still feeling a disturbance in the force.

Geonosis

Four Venators landed on the surface of the planet, behind a large rock formation. Gunships flew from the hangers, roughly ten. One carried three Jedi Masters. The Transports flew in a tight formation, resembling a diamond. They traveled far across the surface, over canyons and mountains

"General Mundi, we have a transmission from _Green one_." A trooper reported

"Put him through"

A clone pilot appeared on the projector

"We are nearing the objective sir. Scanners detect no life"

"Thank you Captain"

The hologram faded out. Mundi turned to Yoda and Unduli.

"Master Yoda, our reports detect no life. Are you sure you feel it here?" Mundi asked

"Certain I am. Feel the darkness I do"

"I feel it too master" Unduli stated

The gunships kept travelling until they finally found rest, setting down in front of an unusual rock formation. As soon as the blast doors opened, Clones poured out of the transports. They moved with precision, taking up positions behind rocks. Gree and Bacara stood out from the movements.

"I feel it. This place is dark" Mundi stated

"Enter we must"

The small Jedi slowly walked up to the rock. He moved his hands, pulling at the rock. It began to shake as Unduli and Mundi joined in. The rock eventually fell apart, opening an unlit pathway inwards.

The group moved in, with torches on their blasters and helmets. Slowly inching forward into the darkness. There was something irregular about the path. Gree had been to Geonosis and even went down into caves and catacombs, but not like this one.

"It is getting stronger" Mundi quietly whispered to himself

"Strong with darkside this place is. Alert we must be" Yoda Stated

They continued down the path until they encountered a light. They believed it was an exit. They kept going towards it.

They looked down through the window. Hundreds of them. Floating in Bacta tanks. The Jedi were shocked, what were they, why were there so many, how did they get there. Luminara lifted the glass up and pushed it to the side with the force. They jumped down into the large room.

The clones and Jedi looked around the room, snooping about the bacta tanks.

"Master Yoda, who are they?" Luminara asked

There was a pause as he searched for answers

"They are Sith" Yoda responded gravely

"Know them I do. Ancient Dark lords, cloned they were, by Sidious. Use them he will, defeat the Jedi he will try" Worry and panic. Yoda walked towards one of the tanks and raised his walking stick to it

"Darth Nihilus is he. Powerful and very dark. Once dead we thought" He said warily

"I remember him. I once studied the Ancient Sith. He fed off the force, he also killed thousands of Jedi. He is supposed to be buried on Moraband. Where is his armor, his spirit was attached to it" Mundi stated

An atmosphere of fear was in the large room. A large _clank_ sound came from the end of the room. Gree and Duke stumbled into a new room, unlit but light from the main room shone through.

"General Mundi, we found his armor" Gree said gravely

The Jedi inspected the room. Countless lightsabers, armors, and at the center of the back wall, an armor stand. The Jedi fell over to their sides, quickly lifted up by the clones

"Destroy… this place… we must" Yoda uttered

Nihilus' mask stood atop the stand. Moments later the clones carried the Jedi out of the room, not before they placed detonators in it. They left the tunnel, with the Jedi still weak from the encounter.

Inside the room, one of the tanks opened. A humanoid climbed out. Bacta dripped from his body, coughing, panting, and shaking.

"I'm alive…I have…a body" He muttered to himself, looking at his hands

He rushed over to the recently opened room, grabbing a lightsaber. A long smooth shape, with curves going across the shiny and reflective surface. He then rushed to the rear of the room, grabbing a robe, then starring down the mask. He felt the power of it, calling it.

"No"

He then dressed himself in the robes and rushed towards the exit, the same used by the Jedi.

He ran out of the tunnel, blinded by the light, something he has not seen in thousands of years, he encountered dozens of clone troopers and three Jedi Masters, but they had their backs turned. The explosives inside detonated, the inferno engulfed the Bacta tanks killing the Sith clones.

The clones turned, and to their surprise it was Nihilus. His lightsaber hissed. The Jedi turned, but they were still weak, Unduli shrieked. The clones raised their weapons to the Sith Lord.

"Lower your weapon" Bacara ordered, pointing his DC-15S blaster carbine at his head

"What are you?" he asked in confusion. Men covered by green and purple armor, pointing blasters at him certainly scared him

"We are Clone Troopers of the-" He stopped speaking not knowing what or who they serve officially

"I sense you Jedi scum" He suddenly said

"Fear you we do not" Yoda replied

The Sith jumped towards one of the gunships and pulled the pilot out, sending him crashing into the wall. The clones opened fire at the Gunship as it lifted off the ground.

"Alert the Admiral" Mundi ordered

"Yes sir" Bacara and Gree replied in unison

Their LAAT's eventually left the cave, heading back towards the fleet

 _Dantooine_

"Master Kota and I felt something dark in the force. Something ancient" Plo said to the new council. They sat on old stone chairs with a light padding on it. The new chamber was in the centre of the temple, exposed to the light of day coming from the large space in the ceiling.

The rest of the temple was rebuilt, the rooms were refurbished, and a hanger bay was created. An underground base was also built, it held most of the fleet and clone barracks while the rest of the fleet was hid in an outpost on one of the seven moons of the planet which also had a research facility, to develop a cure for the ageing clones, and a Cloning facility.

"Darth Nihilus it is" Yoda said walking into the chamber, flanked by Mundi and Unduli

"He has been dead for thousands of years, how could it be?" Shaak Ti said in confusion

Yoda sat down on his chair, resting from his walk.

"A clone is he. Made by Palpatine, his spirit attaching to the body." He continued

"What of Anakin, Master Kenobi?" Kota asked

"I left him on Mustafar, badly deformed and wounded"

"Kill him you did not?" Yoda asked

"No I did not. It would only bring me into down the same path of the darkside"

The meeting was suddenly interrupted by Rex and Nexu rushing into the chamber.

"Generals, Senator Amidala just went into labor" Rex reported

The council quickly broke off following the Clones to the medical center. They rushed down the corridors, near sprinting. They reached the Medical Bay, finding Kix and several Medical Droids surrounding Padme. She screamed, and then moaned and groaned. Kix left the circle around the table and headed towards the entrance that was blocked off by the Jedi High Council and the Clone Commanders as well as the Senate Guards.

"How is she Kix?" Kenobi asked

"She has lost her will to live. We are doing everything we can to save the twins" He replied

"She is having twins?" A bodiless voice asked

"Yes" He ran back to the table, trying to assist with the birthing

After a few minutes, he removed the first child, crying aloud. It was a good sign. Seconds later, he removed the second child. He carried them to Padme.

"A boy" he said giving the first child to its mother

"Luke" She smiled with tears in her eyes

"And a girl" He said cheerfully

"Leigh" the tears fell and she handed the children back to Kix. She rolled her head over to the side. Her last breath.

The room fell silent.

Hours later

A large group stood in front of Senator Organa's ship, just a few Meters from the temple

"I will take the girl. My wife and I always wanted a girl" Organa stated, proclaiming his adoption of Leigh

"And to Tatooine, Luke will go. Stay with his family there he will, far from the Empire." Yoda stated,

"Commander Zackery and the Senate Guard will go with you Senator Organa" Kenobi stated.

"I will go with to Tatooine, I will watch over Luke" He followed up

Organa's ship and a lone republic cruiser left Dantooine that day. The Clones went underground, hiding until the time was right. The Jedi however stayed on the surface, meditating, and training force sensitives.

"What of Darth Nihilus?" Stass Allie asked

"Confront him we must, Secura and Ti. Find him you must" Yoda stated

"Master Plo, attack the imperial fleet you will, and idea of their strength you will get. Take Ahsoka with."

"Master Mundi, set a base on Yavin IV you will, need it we will"

"Yes Master" The Council said in unison, adjourning and leaving for their respective missions, with their respective clones, who have now being given a cure for their ageing process

Two fleets of Venators left the planet in opposite directions, one Nu-Class Shuttle also left the planet. Hope soon spread across the Order, hope of bringing an end to the Sith once and for all. The Twins were to bring order and peace to the galaxy. The children of the chosen one. A new era was brought to the galaxy, one of hope, something everyone needed…

 **So now we have a new character, a sith lord. One of my personal favorites. I think I am going to start on A New Hope, but this is not the last of What If? I can guarantee you. I have also being thinking of doing a sought of Roman-Greek type adventure story, please give me your input. Please don't forget to review, it only takes one minute**


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